The 4993-bp cryptic plasmid, pMA2, from a cyanobacterium, Microcystis aeruginosa f. aeruginosa Kützing, originally derived from Kasumigaura lake, was completely sequenced and analyzed. Plasmid pMA2 had a unique sequence motif CTTGATT, which was proposed to be a nicking site on the smaller plasmid pMA1 (2287-bp) by the presence of single-stranded DNA susceptible to S1 nuclease. We had detected the occurrence of the single-stranded pMA1 in the living M. aeruginosa cells. This was also the case of pMA2. Thus, we suggest that both plasmids, pMA1 and pMA2, replicate through the rolling circle mechanism. By computer analysis of the pMA2 sequence, two open reading frames were found: one had a predicted molecular size of 30,440 Da and the other on a complementary one had a predicted molecular size of 10,852 Da. No rep protein was detected. Replication mechanisms of the plasmids are discussed.